6TTU

Ubiquitin Ligation to substrate by a cullin-RING E3 ligase at 3.7A resolution: NEDD8-CUL1-RBX1 N98R-SKP1-monomeric b-TRCP1dD-IkBa-UB~UBE2D2

Functional Information from GO Data

Chain	GOid	namespace	contents
C	0000045	biological_process	autophagosome assembly
C	0000082	biological_process	G1/S transition of mitotic cell cycle
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0005886	cellular_component	plasma membrane
C	0006511	biological_process	ubiquitin-dependent protein catabolic process
C	0006513	biological_process	protein monoubiquitination
C	0006915	biological_process	apoptotic process
C	0007040	biological_process	lysosome organization
C	0008283	biological_process	cell population proliferation
C	0009887	biological_process	animal organ morphogenesis
C	0010507	biological_process	negative regulation of autophagy
C	0010508	biological_process	positive regulation of autophagy
C	0016567	biological_process	protein ubiquitination
C	0019005	cellular_component	SCF ubiquitin ligase complex
C	0030674	molecular_function	protein-macromolecule adaptor activity
C	0031146	biological_process	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
C	0031461	cellular_component	cullin-RING ubiquitin ligase complex
C	0031625	molecular_function	ubiquitin protein ligase binding
C	0031669	biological_process	cellular response to nutrient levels
C	0034599	biological_process	cellular response to oxidative stress
C	0038202	biological_process	TORC1 signaling
C	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
C	0043124	biological_process	negative regulation of canonical NF-kappaB signal transduction
C	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
C	0070936	biological_process	protein K48-linked ubiquitination
C	0097193	biological_process	intrinsic apoptotic signaling pathway
C	0140374	biological_process	antiviral innate immune response
C	0160072	molecular_function	ubiquitin ligase complex scaffold activity
C	1904037	biological_process	positive regulation of epithelial cell apoptotic process
C	1904262	biological_process	negative regulation of TORC1 signaling
C	1990452	cellular_component	Parkin-FBXW7-Cul1 ubiquitin ligase complex
D	0000166	molecular_function	nucleotide binding
D	0000209	biological_process	protein polyubiquitination
D	0004842	molecular_function	ubiquitin-protein transferase activity
D	0005515	molecular_function	protein binding
D	0005524	molecular_function	ATP binding
D	0005634	cellular_component	nucleus
D	0005654	cellular_component	nucleoplasm
D	0005829	cellular_component	cytosol
D	0006511	biological_process	ubiquitin-dependent protein catabolic process
D	0016567	biological_process	protein ubiquitination
D	0016740	molecular_function	transferase activity
D	0032991	cellular_component	protein-containing complex
D	0036211	biological_process	protein modification process
D	0051865	biological_process	protein autoubiquitination
D	0061630	molecular_function	ubiquitin protein ligase activity
D	0061631	molecular_function	ubiquitin conjugating enzyme activity
D	0070062	cellular_component	extracellular exosome
D	0070936	biological_process	protein K48-linked ubiquitination
N	0005515	molecular_function	protein binding
N	0005634	cellular_component	nucleus
N	0005654	cellular_component	nucleoplasm
N	0005737	cellular_component	cytoplasm
N	0005829	cellular_component	cytosol
N	0006357	biological_process	regulation of transcription by RNA polymerase II
N	0006508	biological_process	proteolysis
N	0006511	biological_process	ubiquitin-dependent protein catabolic process
N	0008104	biological_process	intracellular protein localization
N	0009653	biological_process	anatomical structure morphogenesis
N	0016567	biological_process	protein ubiquitination
N	0019941	biological_process	modification-dependent protein catabolic process
N	0030162	biological_process	regulation of proteolysis
N	0031386	molecular_function	protein tag activity
N	0031625	molecular_function	ubiquitin protein ligase binding
N	0036211	biological_process	protein modification process
N	0045116	biological_process	protein neddylation
N	0070062	cellular_component	extracellular exosome
N	0072757	biological_process	cellular response to camptothecin
N	0098794	cellular_component	postsynapse
N	0098978	cellular_component	glutamatergic synapse
N	0150052	biological_process	regulation of postsynapse assembly
R	0000209	biological_process	protein polyubiquitination
R	0004842	molecular_function	ubiquitin-protein transferase activity
R	0005634	cellular_component	nucleus
R	0005654	cellular_component	nucleoplasm
R	0005737	cellular_component	cytoplasm
R	0005829	cellular_component	cytosol
R	0006283	biological_process	transcription-coupled nucleotide-excision repair
R	0006511	biological_process	ubiquitin-dependent protein catabolic process
R	0006513	biological_process	protein monoubiquitination
R	0007283	biological_process	spermatogenesis
R	0008270	molecular_function	zinc ion binding
R	0016567	biological_process	protein ubiquitination
R	0019005	cellular_component	SCF ubiquitin ligase complex
R	0030163	biological_process	protein catabolic process
R	0031146	biological_process	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
R	0031461	cellular_component	cullin-RING ubiquitin ligase complex
R	0031462	cellular_component	Cul2-RING ubiquitin ligase complex
R	0031463	cellular_component	Cul3-RING ubiquitin ligase complex
R	0031464	cellular_component	Cul4A-RING E3 ubiquitin ligase complex
R	0031465	cellular_component	Cul4B-RING E3 ubiquitin ligase complex
R	0031466	cellular_component	Cul5-RING ubiquitin ligase complex
R	0031467	cellular_component	Cul7-RING ubiquitin ligase complex
R	0031625	molecular_function	ubiquitin protein ligase binding
R	0032436	biological_process	positive regulation of proteasomal ubiquitin-dependent protein catabolic process
R	0032480	biological_process	negative regulation of type I interferon production
R	0034450	molecular_function	ubiquitin-ubiquitin ligase activity
R	0034599	biological_process	cellular response to oxidative stress
R	0034644	biological_process	cellular response to UV
R	0042110	biological_process	T cell activation
R	0043123	biological_process	positive regulation of canonical NF-kappaB signal transduction
R	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
R	0045116	biological_process	protein neddylation
R	0045732	biological_process	positive regulation of protein catabolic process
R	0046627	biological_process	negative regulation of insulin receptor signaling pathway
R	0046872	molecular_function	metal ion binding
R	0061629	molecular_function	RNA polymerase II-specific DNA-binding transcription factor binding
R	0061630	molecular_function	ubiquitin protein ligase activity
R	0061663	molecular_function	NEDD8 ligase activity
R	0070936	biological_process	protein K48-linked ubiquitination
R	0071230	biological_process	cellular response to amino acid stimulus
R	0080008	cellular_component	Cul4-RING E3 ubiquitin ligase complex
R	0097602	molecular_function	cullin family protein binding
R	0140627	biological_process	ubiquitin-dependent protein catabolic process via the C-end degron rule pathway
R	0160240	biological_process	RNA polymerase II transcription initiation surveillance
R	1902499	biological_process	positive regulation of protein autoubiquitination
R	1902883	biological_process	negative regulation of response to oxidative stress
R	1904263	biological_process	positive regulation of TORC1 signaling
S	0000209	biological_process	protein polyubiquitination
S	0005515	molecular_function	protein binding
S	0005634	cellular_component	nucleus
S	0005654	cellular_component	nucleoplasm
S	0005737	cellular_component	cytoplasm
S	0005813	cellular_component	centrosome
S	0005829	cellular_component	cytosol
S	0006338	biological_process	chromatin remodeling
S	0006511	biological_process	ubiquitin-dependent protein catabolic process
S	0006513	biological_process	protein monoubiquitination
S	0006915	biological_process	apoptotic process
S	0008013	molecular_function	beta-catenin binding
S	0016567	biological_process	protein ubiquitination
S	0019005	cellular_component	SCF ubiquitin ligase complex
S	0019904	molecular_function	protein domain specific binding
S	0031146	biological_process	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
S	0031467	cellular_component	Cul7-RING ubiquitin ligase complex
S	0031519	cellular_component	PcG protein complex
S	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
S	0051457	biological_process	maintenance of protein location in nucleus
S	0061564	biological_process	axon development
S	0070936	biological_process	protein K48-linked ubiquitination
S	0097602	molecular_function	cullin family protein binding
S	0140677	molecular_function	molecular function activator activity
S	0160072	molecular_function	ubiquitin ligase complex scaffold activity
S	1904037	biological_process	positive regulation of epithelial cell apoptotic process
S	1990444	molecular_function	F-box domain binding
S	1990756	molecular_function	ubiquitin-like ligase-substrate adaptor activity
S	1990757	molecular_function	ubiquitin ligase activator activity
T	0000045	biological_process	autophagosome assembly
T	0000122	biological_process	negative regulation of transcription by RNA polymerase II
T	0000209	biological_process	protein polyubiquitination
T	0005515	molecular_function	protein binding
T	0005634	cellular_component	nucleus
T	0005654	cellular_component	nucleoplasm
T	0005737	cellular_component	cytoplasm
T	0005829	cellular_component	cytosol
T	0006470	biological_process	protein dephosphorylation
T	0006511	biological_process	ubiquitin-dependent protein catabolic process
T	0007040	biological_process	lysosome organization
T	0007165	biological_process	signal transduction
T	0008013	molecular_function	beta-catenin binding
T	0010507	biological_process	negative regulation of autophagy
T	0010508	biological_process	positive regulation of autophagy
T	0016055	biological_process	Wnt signaling pathway
T	0016567	biological_process	protein ubiquitination
T	0016874	molecular_function	ligase activity
T	0019005	cellular_component	SCF ubiquitin ligase complex
T	0030163	biological_process	protein catabolic process
T	0031146	biological_process	SCF-dependent proteasomal ubiquitin-dependent protein catabolic process
T	0031648	biological_process	protein destabilization
T	0031669	biological_process	cellular response to nutrient levels
T	0033598	biological_process	mammary gland epithelial cell proliferation
T	0038061	biological_process	non-canonical NF-kappaB signal transduction
T	0038202	biological_process	TORC1 signaling
T	0042752	biological_process	regulation of circadian rhythm
T	0042753	biological_process	positive regulation of circadian rhythm
T	0043122	biological_process	regulation of canonical NF-kappaB signal transduction
T	0043161	biological_process	proteasome-mediated ubiquitin-dependent protein catabolic process
T	0045309	molecular_function	protein phosphorylated amino acid binding
T	0045862	biological_process	positive regulation of proteolysis
T	0045879	biological_process	negative regulation of smoothened signaling pathway
T	0045893	biological_process	positive regulation of DNA-templated transcription
T	0046983	molecular_function	protein dimerization activity
T	0048511	biological_process	rhythmic process
T	0050852	biological_process	T cell receptor signaling pathway
T	0050860	biological_process	negative regulation of T cell receptor signaling pathway
T	0050862	biological_process	positive regulation of T cell receptor signaling pathway
T	0051726	biological_process	regulation of cell cycle
T	0060444	biological_process	branching involved in mammary gland duct morphogenesis
T	0060828	biological_process	regulation of canonical Wnt signaling pathway
T	0061136	biological_process	regulation of proteasomal protein catabolic process
T	0061630	molecular_function	ubiquitin protein ligase activity
T	0070534	biological_process	protein K63-linked ubiquitination
T	0070936	biological_process	protein K48-linked ubiquitination
T	1904262	biological_process	negative regulation of TORC1 signaling
T	1990756	molecular_function	ubiquitin-like ligase-substrate adaptor activity
T	1990757	molecular_function	ubiquitin ligase activator activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	binding site for residue ZN R 201

Chain	Residue
R	CYS42
R	CYS45
R	HIS80
R	CYS83

---

site_id	AC2
Number of Residues	4
Details	binding site for residue ZN R 202

Chain	Residue
R	CYS75
R	HIS77
R	CYS94
R	ASP97

---

site_id	AC3
Number of Residues	4
Details	binding site for residue ZN R 203

Chain	Residue
R	CYS56
R	CYS68
R	HIS82
R	CYS53

---

Functional Information from PROSITE/UniProt

site_id	PS00183
Number of Residues	16
Details	UBC_1 Ubiquitin-conjugating (UBC) active site signature. YHPNInsn.GsICLdiL

Chain	Residue	Details
D	TYR74-LEU89

---

site_id	PS00299
Number of Residues	26
Details	UBIQUITIN_1 Ubiquitin domain signature. KerVeEkegIPpqqQrLIYsGkqmnD

Chain	Residue	Details
N	LYS27-ASP52
U	LYS27-ASP52

---

site_id	PS00678
Number of Residues	15
Details	WD_REPEATS_1 Trp-Asp (WD) repeats signature. IITGssDsTVRVWDV

Chain	Residue	Details
T	ILE356-VAL370
T	MET396-MET410
T	ILE439-THR453
T	VAL479-ILE493
T	ILE519-LEU533
T	ILE568-PHE582

---

site_id	PS01256
Number of Residues	28
Details	CULLIN_1 Cullin family signature. IKkcIdiLIEKeYLeRvdgekdtYsYlA

Chain	Residue	Details
C	ILE749-ALA776

---

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	38
Details	Domain: {"description":"F-box","evidences":[{"source":"PROSITE-ProRule","id":"PRU00080","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	37
Details	Repeat: {"description":"WD 2"}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	37
Details	Repeat: {"description":"WD 3"}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	37
Details	Repeat: {"description":"WD 4"}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	39
Details	Repeat: {"description":"WD 5"}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	36
Details	Repeat: {"description":"WD 6"}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	38
Details	Region: {"description":"Required for down-regulation of SNAI1"}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	1
Details	Modified residue: {"description":"Phosphothreonine","evidences":[{"source":"PubMed","id":"20068231","evidenceCode":"ECO:0007744"},{"source":"PubMed","id":"21406692","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in SUMO1)","evidences":[{"source":"PubMed","id":"25114211","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	60
Details	Domain: {"description":"Cullin neddylation","evidences":[{"evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI11
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in NEDD8)","evidences":[{"source":"PubMed","id":"10597293","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"15537541","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"18805092","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI12
Number of Residues	2
Details	Region: {"description":"Interaction with UBE1C","evidences":[{"source":"PubMed","id":"14690597","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI13
Number of Residues	2
Details	Site: {"description":"Interaction with UBE1C","evidences":[{"source":"PubMed","id":"14690597","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI14
Number of Residues	1
Details	Modified residue: {"description":"(Microbial infection) Deamidated glutamine","evidences":[{"source":"PubMed","id":"20688984","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21903097","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23175788","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"23589306","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"26632597","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI15
Number of Residues	1
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"UniProtKB","id":"P29595","evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI16
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Gly-Lys) (interchain with K-? in acceptor proteins)","evidences":[{"source":"PubMed","id":"38316879","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI17
Number of Residues	7
Details	Binding site: {"evidences":[{"source":"PubMed","id":"11961546","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"38605244","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1LDJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1LDK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1U6G","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2HYE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3DPL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3DQV","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3RTR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4F52","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4P5O","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8Q7H","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8RHZ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI18
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"11961546","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"38605244","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1LDJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1LDK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1U6G","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2HYE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3DPL","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3DQV","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3RTR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4F52","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4P5O","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"7Z8B","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8Q7H","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8RHZ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI19
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"PubMed","id":"11961546","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"38605244","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1LDJ","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1LDK","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"1U6G","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"2HYE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3DQV","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3RTR","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4F52","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4P5O","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8Q7H","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"8RHZ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI20
Number of Residues	1
Details	Active site: {"description":"Glycyl thioester intermediate","evidences":[{"source":"PROSITE-ProRule","id":"PRU00388","evidenceCode":"ECO:0000255"},{"source":"PROSITE-ProRule","id":"PRU10133","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI21
Number of Residues	1
Details	Modified residue: {"description":"Phosphoserine; by IKKA and IKKE","evidences":[{"source":"PubMed","id":"10329681","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"10574930","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"10882136","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"7628694","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"7796813","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"7878466","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8631829","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI22
Number of Residues	1
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin); alternate","evidences":[{"source":"PubMed","id":"10574930","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20347421","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"7479976","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI23
Number of Residues	2
Details	Cross-link: {"description":"Glycyl lysine isopeptide (Lys-Gly) (interchain with G-Cter in ubiquitin)","evidences":[{"source":"PubMed","id":"10574930","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"20347421","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"7479976","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---